Is SUN1 p.Gln93Pro (c.278A>C) pathogenic?

SUN1 p.Gln93Pro (c.278A>C) is classified Benign in SUN1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-08). Low-frequency (popmax 4.95%, afr); Associated with Emery-Dreifuss muscular dystrophy.

What condition is associated with SUN1 p.Gln93Pro (c.278A>C)?

SUN1 p.Gln93Pro (c.278A>C) is associated with Emery-Dreifuss muscular dystrophy (ClinVar).

How common is SUN1 p.Gln93Pro (c.278A>C) in the general population?

SUN1 p.Gln93Pro (c.278A>C) is low-frequency (popmax 4.95%, afr) (gnomAD).

How is Emery-Dreifuss muscular dystrophy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SUN1 p.Gln93Pro

c.278A>C · rs78842948 · VCV461658

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.95%, afr)

Conditions

Emery-Dreifuss muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.322	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 0.64, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 28 kb · p 0.01 · regional, not allelic
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.95% African / African-American · 3,714/75,052 alleles

Filtering AF 4.82% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.76%

Overall 0.28% 4,520/1,614,168 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.95%	20
Remaining individualsnot grpmax-eligible	0.403%	248
Middle Eastern	0.346%	289
Admixed American	0.335%	299
European (non-Finnish)	0.0269%	3,723
South Asian	0.0143%	7,006
Finnishnot grpmax-eligible	0.00313%	32,000

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SUN1
Protein: p.Gln93Pro
Coding: c.278A>C
MANE Select: NM_001130965
dbSNP: rs78842948
Type: single nucleotide variant
Location: chr7:841957 (GRCh38)
Gene constraint: LOEUF 0.712 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.99 · 8 PDB
Residue 93: the 'lmna-binding' region

Full SUN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Emery-Dreifuss muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Emery-Dreifuss muscular dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

SUN1 p.Ala179Thr Uncertain significance ★★ same condition
SUN1 p.Ala203Thr Uncertain significance ★★ same condition
SUN1 p.Ala232Val Uncertain significance ★★ same condition
SUN1 p.Ala236Thr Uncertain significance ★★ same condition
SUN1 p.Ala255Thr Uncertain significance ★★ same condition
SUN1 p.Ala256Val Uncertain significance ★★ same condition
SUN1 p.Ala404Thr Uncertain significance ★★ same condition
SUN1 p.Ala414Thr Uncertain significance ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/sun1-p-gln93pro (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown